Mapping of pathogenic genes or genes expressing specific phenotypes has been accomplished prior to the invention by comparing the genetic polymorphism markers in test subjects and those in control subjects, and then determining whether there is difference between the frequencies of scific alleles in the test and control subjects.
Such methods of analysis of genetic polymorphism markers include detection of restriction fragment length polymorphisms (RFLP); detection of a variable number of tandem repeats (VNTR) which are scatter within the human genome; detection of the presence or absence of microsatellites markers; and detection of the presence or absence of single nucleotide polymorphisms (SNPs). In particular, methods involving detection of SNPs and microsatellites have attracted attention.
However, there are problems with use of SNPs as the genetic polymorphism markers. For example, because the SNPs are single nucleotide replacements on a genome, generally only two alleles exist, and further only those SNPs existing within 5 kb to 10 kb from to be-mapped genes correlate with the gene. Therefore, genome mapping performed using the SNPs as the genetic polymorphism markers requires an enormous amount of SNPs as markers and an analysis thereof.
Microsatellites avoid some of the problems of SNPs. Many alleles exist for a microsatellite genetic polymorphism markers, and microsatellite markers show correlation to a gene even when it is positioned somewhat far from the gene to be mapped. However, use of microsatellite markers is problematic where there are many microsatellite genetic polymorphism markers used, analysis becomes becomes difficult in terms of tremendous time and labor. In addition, when too few microsatellite markers are used, correlation cannot be found and thus causative genes may be overlooked.
Currently, the field is focusing on specifying a genetic mechanism that defines individual phenotypes through collection and comparison of genetic polymorphism information on a group of subjects, and identifying the susceptibility gene for hereditary diseases with multiple factors or phenotypes. However, the conventional methods utilizing microsatellites or SNPs can work for only limited regions and genes in the human genome, and even for the entire chromosome, only low resolution methods can be used. Therefore, there are many cases of neither being able to identify the susceptibility gene nor eliminate the possibility that other genes are involved even if that identification is successful.
There is a need in the field for methods of gene mapping that address these problems. The present invention addresses this need.